Why did a REORG job run against an entire catalog only process 3 of the files, when there are 352 files listed in the catalog ?

Answer:

The majority of the files in the catalog are SAMI/SAME, listed in the CA Mastercat report as type of

EXPLICIT SAM

IMPLICIT SAM

the only clusters the REORG command has processed are the KSDS/ESDS files.

The purpose of the REORG command is to perform VSAM cluster and alternate index reorganizations, so it will redistribute freespace, eliminate CI/CA splits, rebuild alternate index components and perform extent consolidation if OPTION XTC is specified.

As none of this is applicable to SAMI/SAME those files are not processed.